2026-08-04T07:58:26Z https://drops.dagstuhl.de/oai

oai:drops-oai.dagstuhl.de:14674 2024-03-06T10:54:36Z ddc:004 open_access

Molecular Machines from Topological Linkages Breik, Keenan Luchsinger, Austin Soloveichik, David chemical computation mechanical computation bioengineering models of biochemistry molecular machines mechanical linkages generic rigidity Life is built upon amazingly sophisticated molecular machines whose behavior combines mechanical and chemical action. Engineering of similarly complex nanoscale devices from first principles remains an as yet unrealized goal of bioengineering. In this paper we formalize a simple model of mechanical motion (mechanical linkages) combined with chemical bonding. The model has a natural implementation using DNA with double-stranded rigid links, and single-stranded flexible joints and binding sites. Surprisingly, we show that much of the complex behavior is preserved in an idealized topological model which considers solely the graph connectivity of the linkages. We show a number of artifacts including Boolean logic, catalysts, a fueled motor, and chemo-mechanical coupling, all of which can be understood and reasoned about in the topological model. The variety of achieved behaviors supports the use of topological chemical linkages in understanding and engineering complex molecular behaviors. Schloss Dagstuhl – Leibniz-Zentrum für Informatik Keenan Breik and Austin Luchsinger and David Soloveichik 2021 Is Part Of LIPIcs, Volume 205, 27th International Conference on DNA Computing and Molecular Programming (DNA 27) (2021) InProceedings Text doc-type:ResearchArticle publishedVersion application/pdf doi:10.4230/LIPIcs.DNA.27.7 urn:nbn:de:0030-drops-146749 https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.27.7 eng https://creativecommons.org/licenses/by/4.0/legalcode